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When they lie in bed, Root always stays on her own side (the side nearest the door, still so cautious), but on the cusp of sleep reaches across the bed, clasps her hand around Shaw's wrist, fingers on her pulse. Shaw doesn’t think she even realizes she does it (the first night she was back, the first night it happened, Shaw froze at the touch, unused to contact. Root was so careful then, would never have done anything that risked making Shaw uncomfortable (making her run))
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Shaw knows some of what happened while she was gone (a prisoner of a war no one knew about, of the most important war humanity had ever waged):
Knows what Root did. (No specifics - the experience still too raw to ask Root herself and Shaw doesn't want to hear it from anyone else - but Shaw knows better than most what Root is willing to do to get information (to get something she wants))
Knows what Root became. (The way the team still looks at her, equal parts concern and fear (not for themselves, but for anyone standing in Root's way. Collateral damage, and all Shaw can think of is Cyrus Wells and how close he had been to being just that.), but under that, with a grim understanding.)
Knows what Root would have done, if Shaw hadn’t made it out alive. (John looks her in the eye and says “She would have burned the world down to find you. She almost did.” the 'I almost let her' doesn't need to be said. They both know what he did to avenge Carter, both know what Root had done when someone she cared about (someone she loved, and Shaw keeps stuttering around that, even in her own head) was taken from her the first time)
Knows Root's nightmares. (Wakes in the middle of the night to the sound of her crying (crying and whimpering and pleading, twisting herself apart under the covers.) Root startles herself awake and Shaw reaches across the bed to touch her face, to anchor her in the present, a reality where Shaw is here, where Shaw is safe.) They never talk about them in the light of day.
Knows what Root gave up. (Root never looks awed when the Machine speaks to her anymore, never shares humorous facts about passers-by that she has no way of knowing herself, always turns her implant off before she will truly relax.) (Harold tells her of a street corner and a camera and a plea, tells her of 'Sierra Tango Oscar Papa' and the faith he watched shatter before him, tells her of a defeated 'Goodbye Harold'. Tells her of how afraid he had been that in losing Shaw they’d lost Root as well.).
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Shaw had a lot of time to think while she was away, but her mind always went back to Root (Root, Reese, Finch, Root, Fusco, Carter, Root, Bear, Gen. Root, Root, Root.). She knows what that means, knows it in her bones, even if she doesn't feel it the same way other people do, brash and loud. (Dying would've been worth it if it meant Root lived, and that means something too.)
Shaw might be the one that does the protecting, but she wouldn't (couldn't) deny Root this.